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  • e26e5a6b8b Update amulet to use slightly less popular GPU config Kevin Wu 2022-08-16 01:56:25 +00:00
  • d836dfeeb9 amulet updates Kevin Wu 2022-08-16 00:52:53 +00:00
  • e8f658f971 Add GitPython dependency Kevin Wu 2022-08-16 00:40:23 +00:00
  • f84ef12636 Device tweaks Kevin Wu 2022-08-16 00:40:06 +00:00
  • f2a011b6d8 Allow config of GPUs Kevin Wu 2022-08-16 00:32:18 +00:00
  • afc818e5e4 Ignore vscode files Kevin Wu 2022-08-16 00:25:03 +00:00
  • 00c46b89aa Update amulet yaml Kevin Wu 2022-08-16 00:24:19 +00:00
  • 818064ce79 More logging/model saving Kevin Wu 2022-08-16 00:13:41 +00:00
  • a25bf06fd3 Update default params Kevin Wu 2022-08-15 23:56:38 +00:00
  • b25d610bcf Shape bugfix Kevin Wu 2022-08-15 23:47:35 +00:00
  • 25808fc2e0 Bugfix for arg handling Kevin Wu 2022-08-15 23:26:01 +00:00
  • 26dceb6f54 Initial amulet yaml Kevin Wu 2022-08-15 22:34:06 +00:00
  • 648c5865a7 Update environment yml Kevin Wu 2022-08-15 22:00:17 +00:00
  • a05a03aed9 zip the CATH file Kevin Wu 2022-08-15 21:49:04 +00:00
  • c5a9256783 Add amulet ignore Kevin Wu 2022-08-15 20:35:30 +00:00
  • e201975321 Add json of parameters used to train overfitted small models Kevin Wu 2022-08-12 21:52:41 +00:00
  • 3f230b6b17 Support for MLP decoder Kevin Wu 2022-08-12 21:24:31 +00:00
  • c8fcc4253f Implement option of deeper decoder Kevin Wu 2022-08-12 21:11:45 +00:00
  • faef8c97f8 Comprehensive tests for radian smooth L1 loss Kevin Wu 2022-08-12 19:28:22 +00:00
  • 28c8abaf39 Equal support for LR schedulers in HuggingFace transformer Kevin Wu 2022-08-12 18:12:43 +00:00
  • a1fd8987fe Simplify more alpha beta code Kevin Wu 2022-08-12 06:47:56 +00:00
  • 5d065baa24 Set default implementation to huggingface Kevin Wu 2022-08-12 00:19:36 +00:00
  • f5538b36ed Add title Kevin Wu 2022-08-11 22:13:03 +00:00
  • 8c86996d51 Add plot legends Kevin Wu 2022-08-11 22:08:20 +00:00
  • ac1f204cef Bugfix Kevin Wu 2022-08-11 22:07:34 +00:00
  • eb65cd30c2 Bugfix Kevin Wu 2022-08-11 22:06:46 +00:00
  • 4e45e80051 More comprehensive variance plots Kevin Wu 2022-08-11 22:03:06 +00:00
  • fa67d995f0 Simplify code for getting time-based synthetic noiser Kevin Wu 2022-08-11 21:51:55 +00:00
  • 85d2d2a64a Basic tests for variance schedules Kevin Wu 2022-08-11 21:19:16 +00:00
  • d3a2645fba Misc. formatting updates Kevin Wu 2022-08-11 20:36:49 +00:00
  • 169c8694d4 Simple CLI plotting Kevin Wu 2022-08-11 20:34:29 +00:00
  • 40ea01cba8 Toggle-able use of timestep to noise positional synthetic noiser Kevin Wu 2022-08-11 19:02:18 +00:00
  • 3424557835 Refactor synthetic positional noiser Kevin Wu 2022-08-11 18:49:24 +00:00
  • 2f7dcf0c4f Add comments Kevin Wu 2022-08-11 18:31:50 +00:00
  • 416011421c Make selected ft configurable Kevin Wu 2022-08-11 18:25:28 +00:00
  • 900d269b52 Code to have a simpler loss plot Kevin Wu 2022-08-11 17:22:32 +00:00
  • a46a88a72d More model cleanup Kevin Wu 2022-08-11 06:13:50 +00:00
  • 449bb6a3cd Fully overfitted results Kevin Wu 2022-08-11 06:13:43 +00:00
  • ded8a24b8d More tests for huggingface implementation Kevin Wu 2022-08-10 23:15:19 +00:00
  • 8dac8477f0 Distribution of sin/cos angles Kevin Wu 2022-08-10 22:59:01 +00:00
  • b77c331d73 Add listing of feature names Kevin Wu 2022-08-10 22:28:19 +00:00
  • eb95eda5fc Calculate sin/cos of angles in CATH dataset Kevin Wu 2022-08-10 21:46:31 +00:00
  • fd76fc073b Clean up huggingface model Kevin Wu 2022-08-10 21:36:35 +00:00
  • 30a31f2b11 Reimplement mask format flipping with additional asserts Kevin Wu 2022-08-10 21:26:47 +00:00
  • 5de2473ecb Bugfix for no out dir Kevin Wu 2022-08-10 21:12:51 +00:00
  • 8e98f4cc0f Test cleanup Kevin Wu 2022-08-10 21:12:36 +00:00
  • 7491d9f5fa Fix tests. Still failing Kevin Wu 2022-08-10 19:49:09 +00:00
  • 85dc42881e Huggingface model test noise invariance Kevin Wu 2022-08-10 19:45:16 +00:00
  • 958e375054 Basic huggingface implementation test Kevin Wu 2022-08-10 19:23:54 +00:00
  • 56ec852c55 Clean up tests Kevin Wu 2022-08-10 19:02:26 +00:00
  • e636169215 Init transformer weights with xavier uniform Kevin Wu 2022-08-10 19:02:03 +00:00
  • 04619e995d Model adjustments. Doesn't change output. Kevin Wu 2022-08-10 18:49:11 +00:00
  • 208b6efbcf Fix tests that were really just numerical precision issues Kevin Wu 2022-08-10 17:44:58 +00:00
  • 3e7312a8af Yet another failing attentoin test Kevin Wu 2022-08-10 06:03:43 +00:00
  • 569f10ddbf Update notebook Kevin Wu 2022-08-10 05:43:07 +00:00
  • 8984bf4491 Test that Guassian Fourier projection works as expectd Kevin Wu 2022-08-10 05:39:53 +00:00
  • 2b8ad93915 Flesh out some positional embedding tests Kevin Wu 2022-08-10 05:34:33 +00:00
  • 7c88a479ea Tests for positional embedding Kevin Wu 2022-08-10 05:28:04 +00:00
  • 5475c6dd0d Add plot of losses when comparing positional embedding Kevin Wu 2022-08-10 04:43:22 +00:00
  • 3f7b450d1e Fix bug where positional embedding was added to batch dimension Kevin Wu 2022-08-10 03:15:02 +00:00
  • c8e428d329 More checks in tests Kevin Wu 2022-08-10 03:14:07 +00:00
  • 6f644e6976 Add failing test for batch shuffle invariance Kevin Wu 2022-08-09 22:47:50 +00:00
  • 4ee896999b Update docs Kevin Wu 2022-08-09 22:35:24 +00:00
  • 9c264ddc29 Add unit tests. Fail on noising masked indices Kevin Wu 2022-08-09 22:19:39 +00:00
  • 60c55ac2b1 Update default params to not be illegal Kevin Wu 2022-08-09 22:12:03 +00:00
  • c9536bf43b Synthetic dataset that noises only masked positions Kevin Wu 2022-08-09 21:33:19 +00:00
  • 8ab3afd26c Improve legibility of plots Kevin Wu 2022-08-09 19:19:45 +00:00
  • 18df19374b Bugfix + doc updates Kevin Wu 2022-08-09 19:19:33 +00:00
  • fe89815496 Support for writing valid preds in pytorch model Kevin Wu 2022-08-09 18:46:03 +00:00
  • 55578e7e10 LR scheduler support Kevin Wu 2022-08-09 06:26:26 +00:00
  • 2689600dd6 Loss logging Kevin Wu 2022-08-09 05:40:24 +00:00
  • 2d9f22918f Misc. Kevin Wu 2022-08-09 01:09:55 +00:00
  • 1f7fbc14d9 More testing Kevin Wu 2022-08-09 00:04:39 +00:00
  • f27bccff65 More tests Kevin Wu 2022-08-08 23:57:54 +00:00
  • 53e80c5bfa Additional test Kevin Wu 2022-08-08 23:54:40 +00:00
  • 1da63b78af Logging Kevin Wu 2022-08-08 23:30:20 +00:00
  • 74e94a534b Bugfix Kevin Wu 2022-08-08 23:27:51 +00:00
  • 1a6db0d7d1 Write current Git version Kevin Wu 2022-08-08 23:25:40 +00:00
  • a2d22695da Controllabe implementation Kevin Wu 2022-08-08 23:06:14 +00:00
  • e2e5f3277b Propert support for regularization in custom implementation Kevin Wu 2022-08-08 22:54:54 +00:00
  • 35aa38c737 Hook pytorch implementation into train script Kevin Wu 2022-08-08 22:49:15 +00:00
  • fd5fde3e25 Fix issue with modelling single value Kevin Wu 2022-08-08 22:27:23 +00:00
  • 49835b78f5 Add docs Kevin Wu 2022-08-08 22:06:59 +00:00
  • 7bfbc9aa3b Additional args Kevin Wu 2022-08-08 21:55:16 +00:00
  • f70d6c16cf Initial implementatoin of non-huggingface encoder Kevin Wu 2022-08-08 20:55:16 +00:00
  • 4485d1b040 Notebook testing that positional embedding can be learned Kevin Wu 2022-08-06 18:08:35 +00:00
  • 45a3e635b8 Support for synthetic noiser and for writing validation preds Kevin Wu 2022-08-05 17:44:04 +00:00
  • b8283ee59d Synthetic noiser that relies on positional informatoin Kevin Wu 2022-08-05 00:31:48 +00:00
  • 70a6c1f658 More fixes Kevin Wu 2022-08-04 23:39:48 +00:00
  • 98364fe018 Bugfix Kevin Wu 2022-08-04 23:33:30 +00:00
  • 51a80b4767 Implement bond dist selector class Kevin Wu 2022-08-04 23:29:39 +00:00
  • f1d1e91a1e More fix Kevin Wu 2022-08-04 21:43:32 +00:00
  • 1e4b0b0735 Fix regularize on circle Kevin Wu 2022-08-04 21:39:52 +00:00
  • eaf36d5187 Regularize on number of predicted turns around circle Kevin Wu 2022-08-04 21:34:31 +00:00
  • b660b7a297 Misc. comments and logging Kevin Wu 2022-08-04 20:56:52 +00:00
  • 0c1ea3028d Configurable variance Kevin Wu 2022-08-04 20:56:42 +00:00
  • 8a69b11797 Enable togging of fixed noise Kevin Wu 2022-08-04 01:18:03 +00:00
  • 52f2719029 Fixed noise for single datasets Kevin Wu 2022-08-04 00:25:56 +00:00
  • e828f43a45 Support configuring dropout Kevin Wu 2022-08-03 23:52:45 +00:00
  • e6ed08781e Minor tweaks on indexing for loss calculation Kevin Wu 2022-08-03 23:48:12 +00:00